Usage

library(ggoncoplot)
library(dplyr, warn.conflicts = FALSE)

Input Data

The input for ggoncoplot is a data.frame with 1 row per mutation. data.frame must contain columns describing the following:

• Gene Symbol

• Sample Identifier

• (optional) mutation type

• (optional) tooltip (character string: what we show on mouse hover over a particular mutation)

These columns can be in any order, and named anything. You define the mapping of your input dataset columns to the required features in the call to ggoncoplot

Minimal Example

# TCGA GBM dataset from TCGAmuations package
gbm_csv <- system.file(package='ggoncoplot', "testdata/GBM_tcgamutations_mc3_maf.csv.gz")
gbm_df <- read.csv(file = gbm_csv, header=TRUE)

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode'
  )

Colour by mutation type

Colour by mutation by specifying col_mutation_type

# TCGA GBM dataset from TCGAmuations package
gbm_csv <- system.file(package='ggoncoplot', "testdata/GBM_tcgamutations_mc3_maf.csv.gz")
gbm_df <- read.csv(file = gbm_csv, header=TRUE)

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification'
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Control which genes are shown

Show top [n] Genes

Show the 4 most frequently mutated genes using topn argument

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification', 
    topn = 4
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Exclude Specific Genes

Lets filter out specific genes, such as TTN and MUC16.

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification', 
    topn = 10,
    genes_to_ignore = c("TTN", "MUC16")
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 9 unique mutation types in input set
#> ℹ 0/9 mutation types were valid SO terms
#> ℹ 9/9 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Gene Subset

lets only show TP53 and TERT

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification', 
    genes_to_include = c('TP53', 'TERT'),
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 6 unique mutation types in input set
#> ℹ 0/6 mutation types were valid SO terms
#> ℹ 6/6 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Custom Tooltip

Lets add a custom tooltip that describes the specific mutation

gbm_df |> 
  mutate(tooltip = paste0(Reference_Allele, ">", Tumor_Seq_Allele2)) |>
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification', 
    col_tooltip = 'tooltip' # We'll specify a custom tooltip based on our new 'tooltip' column
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Note tooltips are html, so if you want to insert a break, just paste in <br>.

Similarly, if you want to make text in the tooltip bold, try "<b>text_to_bold<\b>"

Add margin plots

Gene Barplot

How many samples have mutations in each Gene (optionally coloured by mutation type)

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification',
    draw_gene_barplot = TRUE
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete

Tumour Mutation Burden

How many mutations (total) are in each sample

Not implemented yet: coming soon (https://github.com/selkamand/ggoncoplot/issues/30)

Static Plots

gbm_df |> 
  ggoncoplot(
    col_genes = 'Hugo_Symbol', 
    col_samples = 'Tumor_Sample_Barcode', 
    col_mutation_type = 'Variant_Classification', 
    interactive = FALSE
  )
#> 
#> ── Identify Class ──────────────────────────────────────────────────────────────
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete